Abstract

Pharmacotranscriptomics has become a powerful approach for evaluating the therapeutic efficacy of drugs and discovering new drug targets. Recently, studies of traditional Chinese medicine (TCM) have increasingly turned to high-throughput transcriptomic screens for molecular effects of herbs/ingredients. And numerous studies have examined gene targets for herbs/ingredients, and link herbs/ingredients to various modern diseases. However, there is currently no systematic database organizing these data for TCM. Therefore, we built HERB, a high-throughput experiment- and reference-guided database of TCM, with its Chinese name as BenCaoZuJian. We re-analyzed 6164 gene expression profiles from 1037 high-throughput experiments evaluating TCM herbs/ingredients, and generated connections between TCM herbs/ingredients and 2837 modern drugs by mapping the comprehensive pharmacotranscriptomics dataset in HERB to CMap, the largest such dataset for modern drugs. Moreover, we manually curated 1241 gene targets and 494 modern diseases for 473 herbs/ingredients from 1966 references published recently, and cross-referenced this novel information to databases containing such data for drugs. Together with database mining and statistical inference, we linked 12 933 targets and 28 212 diseases to 7263 herbs and 49 258 ingredients and provided six pairwise relationships among them in HERB. In summary, HERB will intensively support the modernization of TCM and guide rational modern drug discovery efforts. And it is accessible through http://herb.ac.cn/.

中文翻译：

---

HERB：高通量的中药实验和参考指南数据库

摘要

药物转录组学已成为评估药物治疗功效和发现新药物靶标的有力方法。最近，对中药（TCM）的研究已越来越多地转向高通量转录组筛选，以了解草药/成分的分子作用。许多研究已经检查了草药/成分的基因靶标，并将草药/成分与各种现代疾病联系起来。但是，目前还没有系统的数据库为中医组织这些数据。因此，我们建立HERB，一^ h IGH-吞吐量é xperiment-和[R eference制导数据b中医，本名叫本草足健。我们重新分析了1037个评估中药/成分的高通量实验的6164个基因表达谱，并通过将HERB中完整的药物转录组学数据集映射到CMap（最大的现代药物数据集），在中药/成分与2837种现代药物之间建立了联系。此外，我们从最近发表的1966年参考文献中手动为473种草药/成分选择了1241个基因靶标和494种现代疾病，并将该新信息交叉引用到包含此类药物数据的数据库中。结合数据库挖掘和统计推断，我们将12 933个目标和28 212个疾病与7263种草药和49 258种成分关联在一起，并在HERB中提供了六种成对关系。综上所述，HERB将大力支持中药现代化，并指导合理的现代药物发现工作。可以通过http://herb.ac.cn/进行访问。